Summary of Study ST002812
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001759. The data can be accessed directly via it's Project DOI: 10.21228/M8BH9K This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST002812 |
| Study Title | Metabolomic profiling of PMM2-CDG brain organoids - Part 1 |
| Study Summary | PMM2-CDG is a rare inborn error of metabolism caused by deficiency of the PMM enzyme, which leads to impaired protein glycosylation. While the disorder has primarily neurological presentation, there is limited knowledge about the specific brain-related changes that result from PMM deficiency. Utilizing 3D brain organoids derived from individuals with PMM2-CDG, we identified abnormal glucose metabolism in PMM2-CDG organoids, indicating disturbances in metabolic utilization. In this experiment, day 160 organoids were used. |
| Institute | Mayo Clinic |
| Last Name | Radenkovic |
| First Name | Silvia |
| Address | 200 2nd Ave SW Rochester MN, USA |
| radenkovic.silvia@mayo.edu | |
| Phone | 507(77) 6-6107 |
| Submit Date | 2023-08-14 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-08-14 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001759 |
| Project DOI: | doi: 10.21228/M8BH9K |
| Project Title: | Metabolomic profiling of PMM2-CDG brain organoids |
| Project Summary: | PMM2-CDG is a rare inborn error of metabolism caused by deficiency of the PMM enzyme, which leads to impaired protein glycosylation. While the disorder has primarily neurological presentation, there is limited knowledge about the specific brain-related changes that result from PMM deficiency. Utilizing 3D brain organoids derived from individuals with PMM2-CDG, we identified abnormal glucose metabolism in PMM2-CDG organoids, indicating disturbances in metabolic utilization. |
| Institute: | Mayo Clinic |
| Last Name: | Radenkovic |
| First Name: | Silvia |
| Address: | 200 2nd Ave SW Rochester MN |
| Email: | radenkovic.silvia@mayo.edu |
| Phone: | 507(77) 6-6107 |
| Funding Source: | NIH, KU Leuven |
Subject:
| Subject ID: | SU002922 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Genotype Strain: | WT/PMM2-CDG |
| Age Or Age Range: | 5-7 |
| Gender: | Male and female |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype |
|---|---|---|
| SA301988 | S01 (2) | CTR |
| SA301989 | S01 (1) | CTR |
| SA301990 | S01 (5) | CTR |
| SA301991 | S01 (4) | CTR |
| SA301992 | S01 (3) | CTR |
| SA301993 | S01 (15) | PMM2-CDG |
| SA301994 | S01 (14) | PMM2-CDG |
| SA301995 | S01 (13) | PMM2-CDG |
| SA301996 | S01 (17) | PMM2-CDG |
| SA301997 | S01 (16) | PMM2-CDG |
| SA301998 | S01 (9) | PMM2-CDG |
| SA301999 | S01 (7) | PMM2-CDG |
| SA302000 | S01 (6) | PMM2-CDG |
| SA302001 | S01 (8) | PMM2-CDG |
| SA302002 | S01 (10) | PMM2-CDG |
| SA302003 | S01 (11) | PMM2-CDG |
| SA302004 | S01 (12) | PMM2-CDG |
| Showing results 1 to 17 of 17 |
Collection:
| Collection ID: | CO002915 |
| Collection Summary: | Brain were collected at day in vitro 160. Briefly, 5 organoids per cell line were collected and washed three times in DPBS (Gibco). The DPBS was then removed, the organoids flash frozen and kept in -80 °C prior to metabolomics experiments. The metabolites were extracted using two phase extraction protocol. First, the organoids were transferred to lysing matrix tube and 350 µL of ice-cold extraction buffer (80 % MeOH, IS) was added to the sample. Next, the organoids were lyzed with ribolyzer, the lysate transferred to 1.5 mL Eppendorf tube and placed overnight at -80 °C. Further, the samples were centrifuged at 15,000 rpm, 4 °C, 20 min. 100 µL of supernatant was transferred to a fresh Eppendorf tube and 35 µL of ddH20 was added, followed by 800 µL 100% chloroform. The samples were then vortexed and stored at 4 °C overnight. Next, the polar phase was the used for Liquid Chromatography/Mass Spectrometry (LC/MS) |
| Sample Type: | Brain organoids |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002931 |
| Treatment Summary: | NA |
Sample Preparation:
| Sampleprep ID: | SP002928 |
| Sampleprep Summary: | Briefly, 5 organoids per cell line were collected and washed three times in DPBS. The DPBS was then removed, the organoids flash frozen and kept in -80 °C prior to metabolomics experiments. The metabolites were extracted using two phase extraction protocol. First, the organoids were transferred to lysing matrix tube and 350 µL of ice-cold extraction buffer (80 % MeOH, IS) was added to the sample. Next, the organoids were lyzed with ribolyzer, the lysate transferred to 1.5 mL Eppendorf tube and placed overnight at -80 °C. Further, the samples were centrifuged at 15,000 rpm, 4 °C, 20 min. 100 µL of supernatant was transferred to a fresh Eppendorf tube and 35 µL of ddH20 was added, followed by 800 µL 100% chloroform. The samples were then vortexed and stored at 4 °C overnight. Next, the polar phase was the used for Liquid Chromatography/Mass Spectrometry (LC/MS) |
| Processing Storage Conditions: | -80℃ |
| Extract Storage: | -80℃ |
Combined analysis:
| Analysis ID | AN004579 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Waters Acquity |
| Column | Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | NEGATIVE |
| Units | AUC |
Chromatography:
| Chromatography ID: | CH003441 |
| Chromatography Summary: | C18 iP REVERSE PHASE |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um) |
| Column Temperature: | 40 |
| Flow Gradient: | The gradient started with 5% of solvent B and 95% solvent A and remained at 5% B until 2 min post injection. A linear gradient to 37% B was carried out until 7 min and increased to 41% until 14 min. Between 14 and 26 minutes the gradient increased to 95% of B and remained at 95% B for 4 minutes. At 30 min the gradient returned to 5% B. The chromatography was stopped at 40 min |
| Flow Rate: | 0.25 ml/min |
| Solvent A: | 100% water; 10mM tributylamine; 15mM acetic acid |
| Solvent B: | 100% methanol |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004325 |
| Analysis ID: | AN004579 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | El-Maven polly, ThermoFisher Xcalibur, Metabolites were annotated based on the in-house metabolite library- elution time and m/z values |
| Ion Mode: | NEGATIVE |
